Plastid Genomes of Flowering Plants: Essential Principles

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2021 May 24

PMID 34028761

Citations 13

Authors

Tracey A Ruhlman

Robert K Jansen

Affiliations

Soon will be listed here.

Abstract

The plastid genome (plastome ) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy, and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations is allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter, we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and the tools of plastid genetic engineering.

Citing Articles

Phylogenetic position and plastid genome structure of , a mycoheterotrophic genus of Orchidaceae (subtribe Orchidinae) endemic to Vietnam.

Samigullin T, Logacheva M, Averyanov L, Zeng S, Fu L, Nuraliev M Front Plant Sci. 2024; 15:1393225.

PMID: 38855461 PMC: 11157612. DOI: 10.3389/fpls.2024.1393225.

Comparative Analysis of Chloroplast Genomes for the Genus Blume (Magnoliaceae): Molecular Structure and Phylogenetic Evolution.

Li T, Zhang S, Deng Y, Li Y Genes (Basel). 2024; 15(4).

PMID: 38674341 PMC: 11048997. DOI: 10.3390/genes15040406.

Dynamic changes in the plastid and mitochondrial genomes of the angiosperm Corydalis pauciovulata (Papaveraceae).

Park S, An B, Park S BMC Plant Biol. 2024; 24(1):303.

PMID: 38644497 PMC: 11034061. DOI: 10.1186/s12870-024-05025-4.

Intrageneric structural variation in organelle genomes from the genus (Apiaceae): genome rearrangement and mitochondrion-to-plastid DNA transfer.

Park S, Park S Front Plant Sci. 2023; 14:1283292.

PMID: 38116150 PMC: 10728875. DOI: 10.3389/fpls.2023.1283292.

More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae).

Kohler M, Reginato M, Jin J, Majure L Ann Bot. 2023; 132(4):771-786.

PMID: 37467174 PMC: 10799996. DOI: 10.1093/aob/mcad098.

References

Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T . Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci U S A. 2002; 99(19):12246-51. PMC: 129430. DOI: 10.1073/pnas.182432999. View

Timmis J, Ayliffe M, Huang C, Martin W . Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet. 2004; 5(2):123-35. DOI: 10.1038/nrg1271. View

Stegemann S, Hartmann S, Ruf S, Bock R . High-frequency gene transfer from the chloroplast genome to the nucleus. Proc Natl Acad Sci U S A. 2003; 100(15):8828-33. PMC: 166398. DOI: 10.1073/pnas.1430924100. View

Sheppard A, Madesis P, Lloyd A, Day A, Ayliffe M, Timmis J . Introducing an RNA editing requirement into a plastid-localised transgene reduces but does not eliminate functional gene transfer to the nucleus. Plant Mol Biol. 2011; 76(3-5):299-309. DOI: 10.1007/s11103-011-9764-2. View

Jansen R, Cai Z, Raubeson L, Daniell H, dePamphilis C, Leebens-Mack J . Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci U S A. 2007; 104(49):19369-74. PMC: 2148296. DOI: 10.1073/pnas.0709121104. View

Wu C, Lai Y, Lin C, Wang Y, Chaw S . Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy. Mol Phylogenet Evol. 2009; 52(1):115-24. DOI: 10.1016/j.ympev.2008.12.026. View

Cai Z, Penaflor C, Kuehl J, Leebens-Mack J, Carlson J, dePamphilis C . Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol Biol. 2006; 6:77. PMC: 1626487. DOI: 10.1186/1471-2148-6-77. View

Kuroda H, Maliga P . The plastid clpP1 protease gene is essential for plant development. Nature. 2003; 425(6953):86-9. DOI: 10.1038/nature01909. View

Kode V, Mudd E, Iamtham S, Day A . The tobacco plastid accD gene is essential and is required for leaf development. Plant J. 2005; 44(2):237-44. DOI: 10.1111/j.1365-313X.2005.02533.x. View

10.

Cronan Jr J, Waldrop G . Multi-subunit acetyl-CoA carboxylases. Prog Lipid Res. 2002; 41(5):407-35. DOI: 10.1016/s0163-7827(02)00007-3. View

11.

Cauz-Santos L, Munhoz C, Rodde N, Cauet S, Santos A, Penha H . The Chloroplast Genome of (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales. Front Plant Sci. 2017; 8:334. PMC: 5345083. DOI: 10.3389/fpls.2017.00334. View

12.

Park S, Ruhlman T, Weng M, Hajrah N, Sabir J, Jansen R . Contrasting Patterns of Nucleotide Substitution Rates Provide Insight into Dynamic Evolution of Plastid and Mitochondrial Genomes of Geranium. Genome Biol Evol. 2017; 9(6):1766-1780. PMC: 5570028. DOI: 10.1093/gbe/evx124. View

13.

Gurdon C, Maliga P . Two distinct plastid genome configurations and unprecedented intraspecies length variation in the accD coding region in Medicago truncatula. DNA Res. 2014; 21(4):417-27. PMC: 4131835. DOI: 10.1093/dnares/dsu007. View

14.

Lee S, Jeong W, Bae J, Bang J, Liu J, Harn C . Characterization of the plastid-encoded carboxyltransferase subunit (accD) gene of potato. Mol Cells. 2004; 17(3):422-9. View

15.

Konishi T, Shinohara K, Yamada K, Sasaki Y . Acetyl-CoA carboxylase in higher plants: most plants other than gramineae have both the prokaryotic and the eukaryotic forms of this enzyme. Plant Cell Physiol. 1996; 37(2):117-22. DOI: 10.1093/oxfordjournals.pcp.a028920. View

16.

Magee A, Aspinall S, Rice D, Cusack B, Semon M, Perry A . Localized hypermutation and associated gene losses in legume chloroplast genomes. Genome Res. 2010; 20(12):1700-10. PMC: 2989996. DOI: 10.1101/gr.111955.110. View

17.

Sabir J, Schwarz E, Ellison N, Zhang J, Baeshen N, Mutwakil M . Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes. Plant Biotechnol J. 2014; 12(6):743-54. DOI: 10.1111/pbi.12179. View

18.

Page M, Hamel P, Gabilly S, Zegzouti H, Perea J, Alonso J . A homolog of prokaryotic thiol disulfide transporter CcdA is required for the assembly of the cytochrome b6f complex in Arabidopsis chloroplasts. J Biol Chem. 2004; 279(31):32474-82. DOI: 10.1074/jbc.M404285200. View

19.

Hamel P, Dreyfuss B, Xie Z, Gabilly S, Merchant S . Essential histidine and tryptophan residues in CcsA, a system II polytopic cytochrome c biogenesis protein. J Biol Chem. 2002; 278(4):2593-603. DOI: 10.1074/jbc.M208651200. View

20.

Sasaki Y, Sekiguchi K, Nagano Y, Matsuno R . Chloroplast envelope protein encoded by chloroplast genome. FEBS Lett. 1993; 316(1):93-8. DOI: 10.1016/0014-5793(93)81743-j. View